I've seen that too, but no idea how to book it on Agoda. When I tried, I got quoted a normal room rate and not a package. I know that there are other hotels with much easier processes directly via their website, but I really wanted this specific hotel.
The package that you are talking about is called "test&go," and it is especially for the Thailand Pass. I would be shocked if it's not going to be accepted.
Also, I advise everyone to check the refund policy of the hotels before booking. Many give you a refund if you don't succeed in getting a Thailand Pass, but some don't.